The mechanism of genotoxicity of the individual and combined pesticides of terbufos and fenthion were evaluated using HepG2 cells and zebrafish embryos. We determined genotoxicity by neutral comet assay and phosphorylation of H2AX (γH2AX), which indicated that cells treated with terbufos and/or fenthion caused DNA double-strand breaks (DSBs). The combination of these pesticides at the equimolar concentration (40 μM) exhibited less toxicity, genotoxicity, and did not impact DNA homologous recombination (HR) repair activity compare to terbufos or fenthion alone treatment. In HepG2 cells, terbufos, fenthion and their combination decreased only Xrcc2 expression (one of DNA HR repair genes). Moreover, the combined pesticides decreased Xrcc6 expression (one of DNA non-homologous end joining (NHEJ) repair genes). In addition, only terbufos or fenthion decreased XRCC2 protein expression, while Ku70 was impacted in all of the treated cells irrespective of up or down regulation. In zebrafish embryos, only fenthion impaired HR genes (Rad51 and Rad18) expression at 24 h. After 48 h exposure to pesticides, the combined pesticides elevated HR genes (Rad51 and Xrcc2) expression while terbufos or fenthion inhibited the expression of these four genes (Rad51, Rad18, Xrcc2, Xrcc6). In addition, the hatching rate of zebrafish embryos with fenthion or the combined pesticide at 72 hpf was significantly impaired. Collectively, terbufos and/or fenthion in combining caused DSBs in HepG2 cells and zebrafish embryos. Moreover, the specific mechanism of combined pesticide both HepG2 and zebrafish embryos revealed antagonism interaction.